atom creation is now optional

Change of philosophy: moltemplate now handles the case where atoms are not created. It requires the option -nocheck to render the input deck successfully. This way, moltemplate can create valid input decks for more heterogeneous tasks such as rerun, create_atoms etc.
I verified that the program produces a valid input deck for standard usage, with the "new MOLECULE" command invoked.

This change generalizes the kinds of files that moltemplate.sh can create.

Thanks to Otello Roscioni (hothello) for contributing this change!